Dataset Information

Genomic landscape of human diversity across Madagascar.

ABSTRACT: Although situated ?400 km from the east coast of Africa, Madagascar exhibits cultural, linguistic, and genetic traits from both Southeast Asia and Eastern Africa. The settlement history remains contentious; we therefore used a grid-based approach to sample at high resolution the genomic diversity (including maternal lineages, paternal lineages, and genome-wide data) across 257 villages and 2,704 Malagasy individuals. We find a common Bantu and Austronesian descent for all Malagasy individuals with a limited paternal contribution from Europe and the Middle East. Admixture and demographic growth happened recently, suggesting a rapid settlement of Madagascar during the last millennium. However, the distribution of African and Asian ancestry across the island reveals that the admixture was sex biased and happened heterogeneously across Madagascar, suggesting independent colonization of Madagascar from Africa and Asia rather than settlement by an already admixed population. In addition, there are geographic influences on the present genomic diversity, independent of the admixture, showing that a few centuries is sufficient to produce detectable genetic structure in human populations.

SUBMITTER: Pierron D

PROVIDER: S-EPMC5559028 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Genomic landscape of human diversity across Madagascar.

Pierron Denis D Heiske Margit M Razafindrazaka Harilanto H Rakoto Ignace I Rabetokotany Nelly N Ravololomanga Bodo B Rakotozafy Lucien M-A LM Rakotomalala Mireille Mialy MM Razafiarivony Michel M Rasoarifetra Bako B Raharijesy Miakabola Andriamampianina MA Razafindralambo Lolona L Ramilisonina Fanony Fulgence F Lejamble Sendra S Thomas Olivier O Mohamed Abdallah Ahmed A Rocher Christophe C Arachiche Amal A Tonaso Laure L Pereda-Loth Veronica V Schiavinato Stéphanie S Brucato Nicolas N Ricaut Francois-Xavier FX Kusuma Pradiptajati P Sudoyo Herawati H Ni Shengyu S Boland Anne A Deleuze Jean-Francois JF Beaujard Philippe P Grange Philippe P Adelaar Sander S Stoneking Mark M Rakotoarisoa Jean-Aimé JA Radimilahy Chantal C Letellier Thierry T

Proceedings of the National Academy of Sciences of the United States of America 20170717 32

Although situated ∼400 km from the east coast of Africa, Madagascar exhibits cultural, linguistic, and genetic traits from both Southeast Asia and Eastern Africa. The settlement history remains contentious; we therefore used a grid-based approach to sample at high resolution the genomic diversity (including maternal lineages, paternal lineages, and genome-wide data) across 257 villages and 2,704 Malagasy individuals. We find a common Bantu and Austronesian descent for all Malagasy individuals wi ...[more]

PMID: 28716916

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Project description:Fusarium graminearum is one of the main causal agents of the Fusarium Head Blight, a worldwide disease affecting cereal cultures, whose presence can lead to contaminated grains with chemically stable and harmful mycotoxins. Resistant cultivars and fungicides are frequently used to control this pathogen, and several observations suggest an adaptation of F. graminearum that raises concerns regarding the future of current plant disease management strategies. To understand the genetic basis as well as the extent of its adaptive potential, we investigated the landscape of genomic diversity among six French isolates of F. graminearum, at single-nucleotide resolution using whole-genome re-sequencing.A total of 242,756 high-confidence genetic variants were detected when compared to the reference genome, among which 96% are single nucleotides polymorphisms. One third of these variants were observed in all isolates. Seventy-seven percent of the total polymorphism is located in 32% of the total length of the genome, comprising telomeric/subtelomeric regions as well as discrete interstitial sections, delineating clear variant enriched genomic regions- 7.5 times in average. About 80% of all the F. graminearum protein-coding genes were found polymorphic. Biological functions are not equally affected: genes potentially involved in host adaptation are preferentially located within polymorphic islands and show greater diversification rate than genes fulfilling basal functions. We further identified 29 putative effector genes enriched with non-synonymous effect mutation.Our results highlight a remarkable level of polymorphism in the genome of F. graminearum distributed in a specific pattern. Indeed, the landscape of genomic diversity follows a bi-partite organization of the genome according to polymorphism and biological functions. We measured, for the first time, the level of sequence diversity for the entire gene repertoire of F. graminearum and revealed that the majority are polymorphic. Those assumed to play a role in host-pathogen interaction are discussed, in the light of the subsequent consequences for host adaptation. The annotated genetic variants discovered for this major pathogen are valuable resources for further genetic and genomic studies.

Dataset Information

Genomic landscape of human diversity across Madagascar.

Publications

Genomic landscape of human diversity across Madagascar.

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